Across southern Afghanistan the petals of the poppies have fallen and soon the harvest of the bulbs will be complete. It is then that the new military plan, or "surge" devised by the Isaf commander General Stanley McChrystal will have its more critical test so far.

The Kandahar operation raises two immediate questions – what progress has been achieved by the McChrystal surge so far, and how much now can an effective government in Kabul gain control over key centres such as Kandahar, Khost, and Jalalabad? On these answers will depend not only the viability of the Obama policy towards the region, but the credibility of the Karzai regime, and whether realistically Afghanistan has a reasonable future as a state?

After eight and a half years of on-off international intervention, insurgency and terrorism, the war in Afghanistan is about to hit a major tipping point. I know there have been tipping points before, and doubtless there will be more in the country's tangled narrative, but for the US and UK and their Afghan policy this looks like being a big one.

Before scrutinising the perils and prospects for Kandahar, it's worth trying to assess the McChrystal surge story so far. In December Obama reluctantly agreed to a reinforcement of 30,000 extra US troops, bringing the total US presence in Afghanistan this summer to around 100,000 forces. The full reinforcement with a US marine expeditionary unit won't be complete for another six weeks.

In February US, UK and Afghan forces embarked on Operation Moshtarak to clear Taliban forces from the fertile area of southern Helmand round Marjah. The move was advertised well in advance, to warn the local people and to persuade the Taliban to flee or surrender. Many of them seem to have done neither. They are still in the area, though not in as great a number.

Journeying through Nad e Ali towards Narwah, Marjah and into the Bowlan desert last month, it seemed that Moshtarak is still a work in progress. British and Afghan troops had managed to clear the roads and push the Taliban from wholesale intimidation of the local farmers at night. One base, held by C Company 1st Royal Anglians, claimed to be the most shot at in the district. "We couldn't get four metres out of the gate and we would be shot at or rocketed," a young lieutenant told me.

He said he was still shocked at now being able to patrol round the local village and mosque without incident, and furthermore with villagers coming up to his men to ask for help. But the Taliban are still around. In one village there had been wholesale intimidation of workers going for the "cash for work" scheme whereby workers would be paid $5 for a hard day's manual work. Intercepts had identified a small group of Saudi Taliban recruits trying to attack the workers.

Both the British and American forces have been dishing out funds for quick impact work schemes – the Americans more generously so, which is giving great concern. Though the Americans are now in Marjah, it is far from clear who their interlocutors should be. Colonel Hakim, an Afghan police commander in Bowlan told me he feared "they are paying people who may be working for the Taliban". This has been confirmed by other sources, and supported by a powerful report from Richard Oppel of the New York Times from Marjah earlier this month.

With so much unfinished business in Helmand, it seems slightly demented for British commanders and politicians to argue that the UK's main effort should shift now to Kandahar. The British have made some real gains in regenerating the farming economy in central Helmand, but huge problems such as Sangin remain. Sangin is described in military-speak as "not being on the main effort" while the US planners focus on Marjah and Kandahar. So for the best part of a year three battalions of the Rifles Regiment have been battling it out to bring some sense of stability and development, a future with a smidgen of hope even, to the beleaguered population. It has come at huge cost, more than 50 killed in action, as many seriously injured with "life-changing injuries" and up to 200 with lighter wounds.

The problem with Sangin is that it may not be on the main effort in the minds of the British military planners and directors, but is very much on the main effort of Helmand's wiliest narco-traffickers. As the commander of 3 Rifles Battle Group, Lt Col Nick Kitson, put it as we looked south and east from patrol base Jamila in Sangin last month: "From here we can see a landscape from which about 40% of the global consumption of heroin is produced."

Which will make Kandahar – its city alone having a population of 1,200,000 – the more difficult. For the British to go there it might be to invite the nightmare of their entanglement in Basra to recur, only 10 times worse.

Kandahar is the place where Mullah Mohammed Omar founded the oldest Afghan strand of the Taliban movement. It is also Karzai country, with the president's brother Ahmed Walid running the district council. He has a spotty record in dealing with both the Taliban and the CIA. The president seems to be getting very afraid about any forthcoming operation in Kandahar. Reports that he told the local elders that he would stop any military operations if they didn't want them seem to be credible.

Even Christina Lamb of the Sunday Times, who has known Hamid Karzai for 22 years, seems to find it hard to explain his latest actions and remarks, let alone defend them.

In the past month he has openly courted President Ahmadinejad of Iran, and made a state visit to China, which hitherto has shown scant interest in his and his state's security. He has also accused foreign powers, meaning the US and its allies, of perpetrating electoral fraud in last year's contentious and corrupt presidential elections. He has said that he might even be driven "to join up with the Taliban".

So the coming operations, once the poppy is in and the Taliban have got their rake-off, raise the question of whether those trying to help Afghanistan rebuild should work with Karzai, round him, or ignore him altogether.

These are the issues on the boil as the Isaf international force alliance is about to launch its "Kandahar operation". We should not expect any answers to them soon. President Obama has set an 18-month deadline on ending the surge of extra troops to Afghanistan, well before the opening of the presidential campaigning season at the end of 2011.

The huge extensions to the runways and barracks at Camp Leatherneck in Helmand and at the Kandahar air base suggest that his commanders seem to know something he may not: that they are going to be in Afghanistan for many years to come.